Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_011382728.1 AMB_RS01425 bifunctional aldolase/short-chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >NCBI__GCF_000009985.1:WP_011382728.1 Length = 679 Score = 371 bits (952), Expect = e-107 Identities = 229/694 (32%), Positives = 358/694 (51%), Gaps = 35/694 (5%) Query: 2 VKHIWDSERAAQL-----PKGVEE----LVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFR 52 +K +W A P+GV VY + L+G D + GGGNTS KTT D Sbjct: 1 MKSLWSDADAESFVTRYAPEGVNRDLALRVYTTRLLGGDPRLVLHGGGNTSCKTTVTDLL 60 Query: 53 GREIEVMWVKGSGSDLATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHP 112 G +EV+ VKGSG D+ ++ ++L + L + D + DE+MVDY +++S P Sbjct: 61 GETVEVLCVKGSGWDMGDIEPAGLPAVRLAPLLKLRRLDSLSDEDMVDYQRGNLMNSASP 120 Query: 113 RPSIETLLHAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSK 172 PS+ETLLH FLP+K +DHTH A++S+ +G+ +A ++YG R +VPY+ PGF L+K Sbjct: 121 NPSVETLLHGFLPHKFIDHTHSTAVLSLVDQPDGEALAREVYGTRMGYVPYIMPGFALAK 180 Query: 173 MIAEGVANNPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGK 232 AE +P E +++ KHG+ T+ + + T Y+ I ++ AEQ + G Sbjct: 181 KAAEIYEQDPTVEGLILVKHGIFTFADNARTAYELMIEMVTLAEQRLEKGRKPLVAATGL 240 Query: 233 RYQPLPEDKRKQILAGIMPVIRGAVSE-EKKMILSYDDHDDVLEFVNSVQAPALSQIGAA 291 P P LA + P++RG ++ K+ IL + + + +V+ + SQ G Sbjct: 241 PKDPAP-------LAEVAPILRGLLANGPKRRILDFRTSNAIRAYVDGAEIGRYSQQGVV 293 Query: 292 CPDHLVHTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQQDGDQI---F 348 PDH + TK P+ + PE + A+ ++ +E+F ++Y AYF+RN Q I Sbjct: 294 TPDHTIRTKNWPVVLP-APEAGKTAEWAEAAQAAIESFEAKYHAYFSRNNQRLGNIKTEL 352 Query: 349 ESAPRVILIPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEY 408 + P V L+PG+G+ G S + ++ + + + A A+G+F + E + + +EY Sbjct: 353 DPKPCVALVPGLGLFGIGASAKDAAIAADIAVNTVESITDAEAIGRFEPVGEADLFDLEY 412 Query: 409 WPLELYKLTLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNIEGAQKIA 468 W LE KL A E +R+V ++TGG GIG+A + FA EG V V D + + A K A Sbjct: 413 WSLEQAKLGKA-AEKPLARQVVVVTGGGSGIGAATAKAFAKEGAEVAVLDRDADAAAKAA 471 Query: 469 GEINDAYGKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATSSPFDETSLK 528 G+A+ + DVT V++AF+R A +GG+D+VV+NAG A E Sbjct: 472 KACG-----GKALGIACDVTDPASVRAAFDRVAERFGGVDVVVSNAGAAWQGAVGEVDDS 526 Query: 529 EWNLNMNVLGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAGKNASAYSSVKALETH 588 + + G+ VA+ A + K Q GG+++F SK +V GKN Y KA Sbjct: 527 TLRASFELNFFGHQAVAQNAVRVFKAQGTGGALLFNASKQAVNPGKNFGPYGLPKAATLF 586 Query: 589 LARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEHYRKRTAL 648 L + A + G+ GIR N+V D + G + + R++A G+ E+ Y L Sbjct: 587 LMKQYALDHGKDGIRSNAVNADRIRSG--LLTDDMIKSRSSARGLS----EQDYMGGNLL 640 Query: 649 LVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGG 682 + ED+A+A + A KA K T C +TVDGG Sbjct: 641 GREVTAEDVADAFVWLA--KASKVTACTVTVDGG 672 Lambda K H 0.317 0.134 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 967 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 689 Length of database: 679 Length adjustment: 39 Effective length of query: 650 Effective length of database: 640 Effective search space: 416000 Effective search space used: 416000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory